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- PDB-7lqp: Rapid development of potent inhibitors of the HIV integrase-LEDGF... -

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Basic information

Entry
Database: PDB / ID: 7lqp
TitleRapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening
ComponentsIntegrase
KeywordsTRANSFERASE/INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


RNA stem-loop binding / DNA integration / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / zinc ion binding
Similarity search - Function
Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core ...Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
IODIDE ION / Chem-YAV / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionFeb 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,41021
Polymers35,7152
Non-polymers2,69519
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-198 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.421, 46.421, 137.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Integrase /


Mass: 17857.289 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 57-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76353
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-YAV / 2-[2-[2-[3-[2-[2-[2-[[3-[2-[3-(2-hydroxy-2-oxoethyl)-5-methyl-1-benzofuran-2-yl]ethynyl]phenyl]carbonylamino]ethoxy]ethoxy]ethylcarbamoyl]phenyl]ethynyl]-5-methyl-1-benzofuran-3-yl]ethanoic acid


Mass: 780.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H40N2O10 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.91 % / Description: Bi-pyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate, 100 mM sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9775 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2.07→46.42 Å / Num. obs: 17645 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 2.07→2.13 Å / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1300 / CC1/2: 0.613 / Rpim(I) all: 0.352

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.07→38.52 Å / Cross valid method: THROUGHOUT / σ(F): 13.15 / Phase error: 24.64 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2386 3423 9.87 %
Rwork0.1786 --
obs0.196 17645 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 124 75 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042369
X-RAY DIFFRACTIONf_angle_d0.7553205
X-RAY DIFFRACTIONf_dihedral_angle_d20.304315
X-RAY DIFFRACTIONf_chiral_restr0.044353
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.35291480.30141419X-RAY DIFFRACTION77
2.11-2.150.28561690.27371490X-RAY DIFFRACTION90
2.15-2.190.28981790.26071621X-RAY DIFFRACTION90
2.19-2.230.33031700.25171534X-RAY DIFFRACTION90
2.23-2.280.32121660.261574X-RAY DIFFRACTION90
2.28-2.330.34571680.25131609X-RAY DIFFRACTION90
2.33-2.390.36171720.23391519X-RAY DIFFRACTION90
2.39-2.460.2531740.21211621X-RAY DIFFRACTION90
2.46-2.530.25651700.21961557X-RAY DIFFRACTION90
2.53-2.610.2381760.21291576X-RAY DIFFRACTION90
2.61-2.70.29571760.20381560X-RAY DIFFRACTION90
2.71-2.810.24281760.1961564X-RAY DIFFRACTION90
2.81-2.940.27431670.18581606X-RAY DIFFRACTION91
2.94-3.10.24051820.17971585X-RAY DIFFRACTION90
3.1-3.290.25441640.18691561X-RAY DIFFRACTION90
3.29-3.540.23951720.16721580X-RAY DIFFRACTION90
3.54-3.90.21211650.14781578X-RAY DIFFRACTION90
3.9-4.460.19481740.14391564X-RAY DIFFRACTION90
4.46-5.620.20751820.1421563X-RAY DIFFRACTION89
5.62-38.520.25921590.20981593X-RAY DIFFRACTION91

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